[gmx-users] simulation of protein in presence of ATP

Tue Jun 23 16:51:35 CEST 2009

OK till here done ! the pdb file generated for EM should have ATP molecule @proper position as input .top file has the ATP.itp included. It did not have. If I do -ci it would randomly replace the solvent. I want ATP @ its proper location. how do i do this ?

________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 23 June, 2009 4:41:22 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> Thanks a lot for kind help. I reached till grompp before minimizing energy of the system where I received an error msg as "Invalid order for directive defaults: ............filename........; line x" !!! what is the meaning of this error ? Is it something to do with path variable problem or writing things in improper order ?
> 

Probably, if you've processed your protein with pdb2gmx as well as the ATP molecule, you have two .top files, each of which contains an #include statement for your force field, so you're duplicating these entries.

Without any information about the contents of your .top(s) or how you've actually built things, this is just a guess.

See here:

http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults

-Justin

> Nikhil
> 
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 23 June, 2009 12:35:12 PM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
> 
> nikhil damle wrote:
>  > Hi,
>  >      We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is "atom N not found in residue 1ATP while combining tdb and rtp"
> 
> pdb2gmx tries to cap termini of peptides automatically, but this isn't a peptide. So look at pdb2gmx -h and choose the option that will allow you to interactively choose that no terminal capping needs to take place.
> 
> Mark
> 
>  > ------------------------------------------------------------------------
>  > *From:* Mark Abraham <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  > *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
>  > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
>  >
>  > nikhil damle wrote:
>  >  > Hi,
>  >  >
>  >  >    Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb file attached herewith.
>  >
>  > You've broken the PDB format, which encodes the information in fixed-column style. See http://www.wwpdb.org/documentation/format32/v3.2.html
>  >
>  > Mark
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-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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